Metagenomics is gradually being implemented for diagnosing infectious diseases. However, in-depth protocol comparisons for viral detection have been limited to individual sets of experimental workflows and laboratories. In this study, we present a benchmark of metagenomics protocols used in clinical diagnostic laboratories initiated by the European Society for Clinical Virology (ESCV) Network on NGS (ENNGS). A mock viral reference panel was designed to mimic low biomass clinical specimens. The panel was used to assess the performance of twelve metagenomic wet lab protocols currently in use in the diagnostic laboratories of participating ENNGS member institutions. Both Illumina and Nanopore, shotgun and targeted capture probe protocols were included. Performance metrics sensitivity, specificity, and quantitative potential were assessed using a central bioinformatics pipeline. Overall, viral pathogens with loads down to 104 copies/ml (corresponding to CT values of 31 in our PCR assays) were detected by all the evaluated metagenomic wet lab protocols. In contrast, lower abundant mixed viruses of CT values of 35 and higher were detected only by a minority of the protocols. Considering the reference panel as the gold standard, optimal thresholds to define a positive result were determined per protocol, based on the horizontal genome coverage. Implementing these thresholds, sensitivity and specificity of the protocols ranged from 67 to 100 % and 87 to 100 %, respectively. A variety of metagenomic protocols are currently in use in clinical diagnostic laboratories. Detection of low abundant viral pathogens and mixed infections remains a challenge, implying the need for standardization of metagenomic analysis for use in clinical settings.
- MeSH
- benchmarking * MeSH
- lidé MeSH
- metagenomika * metody normy MeSH
- senzitivita a specificita * MeSH
- virové nemoci diagnóza virologie MeSH
- viry * genetika klasifikace izolace a purifikace MeSH
- výpočetní biologie metody MeSH
- vysoce účinné nukleotidové sekvenování metody normy MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- multicentrická studie MeSH
Cíl: Přehledová práce poskytuje základní praktické informace o využití biosenzorů v rychlé diagnostice virových patogenů. Výsledky: Viry díky evolučním změnám v genomu přeskakují do lidské populace, u níž vyvolávají závažné epidemie. Rychlé diagnostické nástroje POCT založené na biosenzorech umožní jejich rozpoznání pro potřeby klinické diagnostiky mimo specializované laboratoře. Kombinace těchto zařízení s technikami 3D tisku, mikrofluidních systémů, nanotechnologie a elektrochemické detekce výrazně zvyšuje využitelnost biosenzorů v laboratorní medicíně. Intenzivní nanomedicínský výzkum probíhá u celé řady virů, např. HIV, ebola, chřipka a viry hepatitid. V souvislosti s celosvětovou pandemií covid-19 se v současné době vývoj nanobiosenzorů ubírá především směrem k detekci SARS-CoV-2. Závěr: Dostupná literární data naznačují, že rychlé senzory a biosenzory mají značný klinický potenciál pro využití v POCT.
Aim: The review provides basic practical information about the use of biosensors in the rapid diagnosis of viral pathogens. Results: Thanks to evolutionary changes in the genome, viruses jump into the human population, where they cause serious epidemics. Rapid POCT diagnostic tools based on biosensors will enable their use for clinical diagnosis needs outside of specialized laboratories. The combination of these devices with the techniques of 3D printing, microfluidic systems, nanotechnology and electrochemical detection significantly increases the usability of biosensors. Intensive research is carried out on a wide range of viruses, e.g. HIV, Ebola, influenza, hepatitis viruses. In connection with the global covid-19 pandemic, the development of nanobiosensors is currently focused primarily on the detection of SARS-CoV-2. Conclusion: Available literature data suggest that fast sensors and biosensors have considerable clinical potential for the use in POCT.
- MeSH
- biosenzitivní techniky * MeSH
- DNA virů analýza MeSH
- elektrochemie MeSH
- lidé MeSH
- nanomedicína MeSH
- nanotechnologie MeSH
- point of care testing MeSH
- viry * izolace a purifikace MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- přehledy MeSH
Viruses are common causes of food- and waterborne diseases worldwide. Conventional identification of these agents is based on cultivation, antigen detection, electron microscopy, or real-time PCR. Because recent technological advancements in detection methods are focused on fast and robust analysis, a rapid multiplexing technology, which can detect a broad spectrum of pathogenic viruses connected to food or water contamination, was utilized. A new semiquantitative magnetic bead-based multiplex system has been designed for simultaneous detection of several targets in one reaction. The system includes adenoviruses 40/41 (AdV), rotavirus A (RVA), norovirus (NoV), hepatitis E virus (HEV), hepatitis A virus (HAV), and a target for external control of the system. To evaluate the detection system, interlaboratory ring tests were performed in four independent laboratories. Analytical specificity of the tool was tested on a cohort of pathogenic agents and biological samples with quantitative PCR as a reference method. Limit of detection (analytical sensitivity) of 5 × 100 (AdV, HEV, and RVA) and 5 × 101 (HAV and NoV) genome equivalents per reaction was reached. This robust, senstivie, and rapid multiplexing technology may be used to routinely monitor and manage viruses in food and water to prevent food and waterborne diseases.
Our recent experience of the COVID-19 pandemic has highlighted the importance of easy-to-use, quick, cheap, sensitive and selective detection of virus pathogens for the efficient monitoring and treatment of virus diseases. Early detection of viruses provides essential information about possible efficient and targeted treatments, prolongs the therapeutic window and hence reduces morbidity. Graphene is a lightweight, chemically stable and conductive material that can be successfully utilized for the detection of various virus strains. The sensitivity and selectivity of graphene can be enhanced by its functionalization or combination with other materials. Introducing suitable functional groups and/or counterparts in the hybrid structure enables tuning of the optical and electrical properties, which is particularly attractive for rapid and easy-to-use virus detection. In this review, we cover all the different types of graphene-based sensors available for virus detection, including, e.g., photoluminescence and colorimetric sensors, and surface plasmon resonance biosensors. Various strategies of electrochemical detection of viruses based on, e.g., DNA hybridization or antigen-antibody interactions, are also discussed. We summarize the current state-of-the-art applications of graphene-based systems for sensing a variety of viruses, e.g., SARS-CoV-2, influenza, dengue fever, hepatitis C virus, HIV, rotavirus and Zika virus. General principles, mechanisms of action, advantages and drawbacks are presented to provide useful information for the further development and construction of advanced virus biosensors. We highlight that the unique and tunable physicochemical properties of graphene-based nanomaterials make them ideal candidates for engineering and miniaturization of biosensors.
- MeSH
- Betacoronavirus genetika izolace a purifikace patogenita MeSH
- biosenzitivní techniky * přístrojové vybavení metody trendy MeSH
- design vybavení MeSH
- DNA virů analýza genetika MeSH
- elektrochemické techniky MeSH
- grafit * chemie MeSH
- hybridizace nukleových kyselin MeSH
- klinické laboratorní techniky * přístrojové vybavení metody statistika a číselné údaje MeSH
- kolorimetrie MeSH
- koronavirové infekce diagnóza epidemiologie virologie MeSH
- kvantové tečky chemie MeSH
- lidé MeSH
- luminiscence MeSH
- nanostruktury chemie MeSH
- pandemie MeSH
- povrchová plasmonová rezonance MeSH
- Ramanova spektroskopie MeSH
- reakce antigenu s protilátkou MeSH
- virologie metody MeSH
- virová pneumonie diagnóza epidemiologie virologie MeSH
- viry genetika izolace a purifikace patogenita MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- přehledy MeSH
Instrumental insemination of Apis mellifera L. queens is a widely employed technique used in honeybee breeding that enables the effective control of mating. However, drone semen represents a potential source of honeybee viruses. In this study, 43 semen doses collected from apparently healthy drones, and consequently used in instrumental insemination, were analysed using PCR or RT-PCR to detect the presence of viral genome of 11 honeybee viruses. In 91% of samples, viral infection was detected. The survey revealed genomes of five viruses, namely Deformed wing virus (DWV), Acute bee paralysis virus (ABPV), Black queen cell virus (BQCV), Sacbrood virus (SBV), and A. mellifera filamentous virus (AmFV) in 84%, 19%, 14%, 2%, and 67% of samples, respectively. Single infection (30% of samples) as well as multiple infection (61% of samples) of two, three or four pathogens were also evaluated. To the best of our knowledge, this is the first study describing the presence of the BQCV and SBV genome sequence in drone ejaculate. Phylogenetic analysis of BQCV partial helicase gene sequence revealed the high similarity of nucleotide sequence of described Czech strains, which varied from 91.4% to 99.6%. The findings of our study indicate the possibility of venereal transmission of BQCV and SBV.
- MeSH
- biodiverzita * MeSH
- chov metody MeSH
- polymerázová řetězová reakce s reverzní transkripcí MeSH
- polymerázová řetězová reakce MeSH
- sperma virologie MeSH
- včely virologie MeSH
- viry klasifikace genetika izolace a purifikace MeSH
- zvířata MeSH
- Check Tag
- mužské pohlaví MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Members of the family Pleolipoviridae (termed pleolipoviruses) are pseudo-spherical and pleomorphic archaeal viruses. The enveloped virion is a simple membrane vesicle, which encloses different types of DNA genomes of approximately 7-16 kbp (or kilonucleotides). Typically, virions contain a single type of transmembrane (spike) protein at the envelope and a single type of membrane protein, which is embedded in the envelope and located in the internal side of the membrane. All viruses infect extremely halophilic archaea in the class Halobacteria (phylum Euryarchaeota). Pleolipoviruses have a narrow host range and a persistent, non-lytic life cycle. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the taxonomy of the Pleolipoviridae which is available at www.ictv.global/report/pleolipoviridae.
This study condenses data acquired during investigations of the virological quality of irrigation water used in production of fresh produce. One hundred and eight samples of irrigation water were collected from five berry fruit farms in Finland (1), the Czech Republic (1), Serbia (2), and Poland (1), and sixty-one samples were collected from three leafy green vegetable farms in Poland, Serbia, and Greece. Samples were analyzed for index viruses of human or animal fecal contamination (human and porcine adenoviruses, and bovine polyoma viruses), and human pathogenic viruses (hepatitis A virus, hepatitis E virus, and noroviruses GI/GII). Both index and pathogenic viruses were found in irrigation water samples from the leafy green vegetables production chain. The data on the presence of index viruses indicated that the highest percentage of fecal contamination was of human origin (28.1 %, 18/64), followed by that of porcine (15.4 %, 6/39) and bovine (5.1 %, 2/39) origins. Hepatitis E virus (5 %, 1/20) and noroviruses GII (14.3 %, 4/28) were also detected. Samples from berry fruit production were also positive for both index and pathogenic viruses. The highest percentage of fecal contamination was of human origin (8.3 %, 9/108), followed by that of porcine, 4.5 % (4/89) and bovine, 1.1 % (1/89) origins. Norovirus GII (3.6 %, 2/56) was also detected. These data demonstrate that irrigation water used in primary production is an important vehicle of viral contamination for fresh produce, and thus is a critical control point which should be integrated into food safety management systems for viruses. The recommendations of Codex Alimentarius, as well as regulations on the use of water of appropriate quality for irrigation purposes, should be followed.
- MeSH
- kontaminace potravin analýza MeSH
- listy rostlin růst a vývoj virologie MeSH
- ovoce růst a vývoj virologie MeSH
- sladká voda chemie virologie MeSH
- viry klasifikace genetika izolace a purifikace MeSH
- zelenina růst a vývoj virologie MeSH
- zemědělské zavlažování MeSH
- Publikační typ
- časopisecké články MeSH
- Geografické názvy
- Evropa MeSH
Rodents are distributed throughout the world and interact with humans in many ways. They provide vital ecosystem services, some species are useful models in biomedical research and some are held as pet animals. However, many rodent species can have adverse effects such as damage to crops and stored produce, and they are of health concern because of the transmission of pathogens to humans and livestock. The first rodent viruses were discovered by isolation approaches and resulted in break-through knowledge in immunology, molecular and cell biology, and cancer research. In addition to rodent-specific viruses, rodent-borne viruses are causing a large number of zoonotic diseases. Most prominent examples are reemerging outbreaks of human hemorrhagic fever disease cases caused by arena- and hantaviruses. In addition, rodents are reservoirs for vector-borne pathogens, such as tick-borne encephalitis virus and Borrelia spp., and may carry human pathogenic agents, but likely are not involved in their transmission to human. In our days, next-generation sequencing or high-throughput sequencing (HTS) is revolutionizing the speed of the discovery of novel viruses, but other molecular approaches, such as generic RT-PCR/PCR and rolling circle amplification techniques, contribute significantly to the rapidly ongoing process. However, the current knowledge still represents only the tip of the iceberg, when comparing the known human viruses to those known for rodents, the mammalian taxon with the largest species number. The diagnostic potential of HTS-based metagenomic approaches is illustrated by their use in the discovery and complete genome determination of novel borna- and adenoviruses as causative disease agents in squirrels. In conclusion, HTS, in combination with conventional RT-PCR/PCR-based approaches, resulted in a drastically increased knowledge of the diversity of rodent viruses. Future improvements of the used workflows, including bioinformatics analysis, will further enhance our knowledge and preparedness in case of the emergence of novel viruses. Classical virological and additional molecular approaches are needed for genome annotation and functional characterization of novel viruses, discovered by these technologies, and evaluation of their zoonotic potential.
- MeSH
- diagnostické techniky molekulární metody MeSH
- hlodavci virologie MeSH
- metagenomika metody MeSH
- techniky amplifikace nukleových kyselin metody MeSH
- virové nemoci epidemiologie veterinární virologie MeSH
- viry klasifikace genetika izolace a purifikace MeSH
- vysoce účinné nukleotidové sekvenování metody MeSH
- zoonózy epidemiologie virologie MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
